[keithwhor]

Degenerate nucleotide matching (using this method) is only possible with 4 bits of data.

If BLAT is using this method for counting matches, I'm unaware. The algorithm is reliant on storing nucleotides in 4 bits, so I doubt it uses this exact method.

[dekhn]

Actually, given huffman coding, you can do it with fewer than 4 because the degenerates are so rare.

[keithwhor]

Kills the algorithm (as described here) performance when you have nonstandard nucleotide widths (in bits). Rather, makes it completely unsuitable. It's dependent upon fixed-width binary data.